water in the sills

I have recently bought a MX5 Roadster, Mk1 soft top, I had water gathering in the sills and on the carpet inside on the floor.  The top is new and the latches fit tighlty.  I have cleaned the rear and front drains thinking this would solve the problem, but I still have water sloshing around in the passenger side sill.  This has been as a result of the recent bad weather.  Any clues what else I can do to stop the water getting in?

 

Gracias, thankyou

El amigo Carlos

 You can not have cleaned the drainage holes, in the sill with water in, properly, try again.